Strain identifier

BacDive ID: 18082

Type strain: No

Species: Flavonifractor plautii

Strain Designation: 265

Strain history: <- V. Bokkenheuser, 265

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 2796

BacDive-ID: 18082

DSM-Number: 6740

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive

description: Flavonifractor plautii 265 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from human faeces.

NCBI tax id

NCBI tax idMatching level
649753strain
292800species

strain history

  • @ref: 2796
  • history: <- V. Bokkenheuser, 265

doi: 10.13145/bacdive18082.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Oscillospiraceae
  • genus: Flavonifractor
  • species: Flavonifractor plautii
  • full scientific name: Flavonifractor plautii (Séguin 1928) Carlier et al. 2010
  • synonyms

    @refsynonym
    20215Fusobacterium plautii
    20215Fusobacterium plauti
    20215Clostridium orbiscindens
    20215Eubacterium plautii

@ref: 2796

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Oscillospiraceae

genus: Flavonifractor

species: Flavonifractor plautii

full scientific name: Flavonifractor plautii (Séguin 1928) Carlier et al. 2010

strain designation: 265

type strain: no

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2796WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339)yeshttps://mediadive.dsmz.de/medium/339Name: WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339) Composition: dehydrated Wilkins-Chalgren medium 33.0 g/l L-Cysteine HCl 0.3 g/l Sodium resazurin 0.0005 g/l Distilled water
2796CHOPPED MEAT MEDIUM (DSMZ Medium 78)yeshttps://mediadive.dsmz.de/medium/78Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water

culture temp

  • @ref: 2796
  • growth: positive
  • type: growth
  • temperature: 37
  • range: mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
2796anaerobe
69480anaerobe99.669

spore formation

@refspore formationconfidence
69481no96
69480no99.455

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase-3.4.11.5
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase-3.2.1.21
68380alpha-glucosidase-3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase-3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
2796-----------------+/----+/--------

Isolation, sampling and environmental information

isolation

  • @ref: 2796
  • sample type: human faeces
  • country: USA
  • origin.country: USA
  • continent: North America

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_447.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_91;96_299;97_331;98_372;99_447&stattab=map
  • Last taxonomy: Flavonifractor plautii subclade
  • 16S sequence: Y18187
  • Sequence Identity:
  • Total samples: 272590
  • soil counts: 1740
  • aquatic counts: 3332
  • animal counts: 266872
  • plant counts: 646

Safety information

risk assessment

  • @ref: 2796
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 2796
  • description: Clostridium orbiscindens 16S rRNA gene, partial, strain DSM 6740
  • accession: Y18187
  • length: 1550
  • database: ena
  • NCBI tax ID: 649753

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavonifractor plautii DSM 6740GCA_004345805scaffoldncbi649753
66792Flavonifractor plautii DSM 6740649753.4wgspatric649753
66792Flavonifractor plautii DSM 67402795385455draftimg649753

GC content

  • @ref: 2796
  • GC-content: 56

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno96no
motileyes76.905no
flagellatedno77.405no
gram-positiveno51.266no
anaerobicyes99.517yes
aerobicno98.522yes
halophileno93.873no
spore-formingyes56.832no
glucose-utilyes86.399no
thermophileno96.208yes
glucose-fermentyes61.569no

External links

@ref: 2796

culture collection no.: DSM 6740, ATCC 49531

straininfo link

  • @ref: 87070
  • straininfo: 42536

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny1883711Clostridium orbiscindens sp. nov., a human intestinal bacterium capable of cleaving the flavonoid C-ring.Winter J, Popoff MR, Grimont P, Bokkenheuser VDInt J Syst Bacteriol10.1099/00207713-41-3-3551991Base Composition, Clostridium/isolation & purification/*metabolism/ultrastructure, DNA, Bacterial/chemistry/metabolism, Feces/microbiology, Flavonoids/genetics/*metabolism, Humans, Intestines/*microbiology, Microscopy, Electron, Molecular Structure, Nucleic Acid HybridizationMetabolism
Phylogeny17684268Oscillibacter valericigenes gen. nov., sp. nov., a valerate-producing anaerobic bacterium isolated from the alimentary canal of a Japanese corbicula clam.Iino T, Mori K, Tanaka K, Suzuki KI, Harayama SInt J Syst Evol Microbiol10.1099/ijs.0.64717-02007Anaerobiosis, Animals, Base Composition, Bivalvia/*microbiology, Clostridium/classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Gastrointestinal Tract/microbiology, Japan, Molecular Sequence Data, RNA, Ribosomal, 16S/genetics, Valerates/metabolismMetabolism
Phylogeny19654357Proposal to unify Clostridium orbiscindens Winter et al. 1991 and Eubacterium plautii (Seguin 1928) Hofstad and Aasjord 1982, with description of Flavonifractor plautii gen. nov., comb. nov., and reassignment of Bacteroides capillosus to Pseudoflavonifractor capillosus gen. nov., comb. nov.Carlier JP, Bedora-Faure M, K'ouas G, Alauzet C, Mory FInt J Syst Evol Microbiol10.1099/ijs.0.016725-02009Bacterial Infections/*microbiology, Bacterial Typing Techniques, Bacteroides/*classification/genetics/isolation & purification, Base Composition, Clostridium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Eubacterium/*classification/genetics/isolation & purification, Humans, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsEnzymology
Metabolism21457417Isolation of catechin-converting human intestinal bacteria.Kutschera M, Engst W, Blaut M, Braune AJ Appl Microbiol10.1111/j.1365-2672.2011.05025.x2011Actinobacteria/*isolation & purification/metabolism, Catechin/*metabolism, Clostridium/*isolation & purification/metabolism, Feces/microbiology, Humans, Intestinal Mucosa/metabolism, Intestines/*microbiologyPhylogeny
Phylogeny24947740Isolation and characterization of rat intestinal bacteria involved in biotransformation of (-)-epigallocatechin.Takagaki A, Kato Y, Nanjo FArch Microbiol10.1007/s00203-014-1006-y2014Actinobacteria/classification/genetics/*isolation & purification/metabolism, Animals, Bacteria/classification/genetics/*isolation & purification/metabolism, Biotransformation, Catechin/*analogs & derivatives/metabolism, Feces/*microbiology, Lactones/metabolism, Metabolic Networks and Pathways, Pentanoic Acids/metabolism, RatsMetabolism
Metabolism25947926Bioconversion of (-)-epicatechin, (+)-epicatechin, (-)-catechin, and (+)-catechin by (-)-epigallocatechin-metabolizing bacteria.Takagaki A, Nanjo FBiol Pharm Bull10.1248/bpb.b14-008132015Actinobacteria/metabolism, Bacteria/*metabolism, *Bioreactors, Biotransformation, Catechin/analogs & derivatives/*metabolism, Clostridium/metabolism, Hydroxylation
Enzymology33542233Discovery of an ene-reductase for initiating flavone and flavonol catabolism in gut bacteria.Yang G, Hong S, Yang P, Sun Y, Wang Y, Zhang P, Jiang W, Gu YNat Commun10.1038/s41467-021-20974-22021Bacterial Proteins/genetics/isolation & purification/*metabolism/ultrastructure, Clostridiales/enzymology/genetics, Crystallography, X-Ray, Flavones/*metabolism, Flavonols/*metabolism, Gastrointestinal Microbiome/*physiology, Oxidoreductases/genetics/isolation & purification/*metabolism/ultrastructure, Phylogeny, Recombinant Proteins/genetics/isolation & purification/metabolism/ultrastructureMetabolism

Reference

@idauthorscataloguedoi/urltitle
2796Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6740)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6740
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
68380Automatically annotated from API rID32A
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
87070Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42536.1StrainInfo: A central database for resolving microbial strain identifiers